Entering edit mode
3.1 years ago
memento1984_1
•
0
Hi All, I was wondering if there is any tool that can correctly visualize long indels (eg known deletions that are 50bp+ long). Bam files were aligned with BWA and vcf calls were done with GATK 3.x I tried to use samtools to extract the range of reads from the final bam (+/- 1000bp) but IGV (2.8.13) does not seem to show the expected junctions. thanks,
could be that abra and indel realignment will help